He will be replaced by Jason Marker, 46, who had led the United States operations of KFC, a fast-food chain owned by Yum Brands.

Mr. Puzder led a turnaround of Carl’s Jr. and Hardee’s, which were struggling amid intense competition from other burger chains when he took over in 2000.

But he was also a contentious figure in the industry, sharply criticizing minimum-wage laws and other regulations imposed on employers. Under his leadership, CKE paid millions of dollars to settle claims that it failed to pay managers fairly, and the company was accused of understaffing its restaurants and forcing employees to work through break periods.

He was also an unabashed defender of his company’s racy television commercials, some of which featured bikini-clad women suggestively mouthing Carl’s Jr. burgers.

“I used to hear, brands take on the personality of the C.E.O.,” he told Entrepreneur magazine. “And I rarely thought that was true, but I think this one, in this case, it kind of did take on my personality.”

After Mr. Trump nominated him to lead the Labor Department, which oversees and enforces many of the nation’s labor regulations, Mr. Puzder admitted that he had employed an undocumented immigrant as a housekeeper for several years and failed to pay the required taxes until much later. During the Senate confirmation process, lawmakers also investigated claims of domestic violence that were made by his ex-wife and later recanted.

With Democratic senators and some Republicans expressing opposition to his nomination, he withdrew his name on Feb. 15 and said he would return to leading CKE.

In a statement on Tuesday, Mr. Puzder offered no explanation for his change of heart. “I expressed my desire to have CKE plan for succession approximately a year ago, and I could not be more pleased to have Jason Marker selected to be the company’s next leader,” he said.

A CKE spokeswoman said that neither Mr. Puzder nor Mr. Marker were available for interviews about the change of leadership at the company, which owns or franchises more than 3,800 restaurants globally.

CKE also declined to comment on whether Mr. Puzder has retained his substantial ownership stake in CKE, which he had planned to sell had he been confirmed to the Labor post.

Mr. Marker, who will begin his new job in April, led KFC’s core American operations for the past three years, overseeing about 4,200 restaurants. Previously, he held other jobs at Yum and at Unilever, a consumer products maker.

A version of this article appears in print on , on Page B3 of the New York edition with the headline: After Failed Bid to Join Cabinet, Puzder Steps Down From Restaurant Post. Order Reprints | Today’s Paper | Subscribe